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You are here: Home Community Minutes Conference Calls 2013 2013-08-06 Tuesday Team Meeting

2013-08-06 Tuesday Team Meeting

Dundee: Chris, Mark, Kenny, Andrew, Gus, Helen, Blazej, Ola, Jason, Jean-Marie, Roger, Simon Remote: Colin, Josh, Douglas, Sebastien B, Mark H, Melissa, Sebastien S, Chris C

Agenda - 2:30pm Start

  1. Accepting minutes from last meeting

    • accepted
  2. Summer testing updates - 14:29 UK

    • CI/Partner Projects (Sebastien)
      • just back from leave
      • working on FLIMfit with Ian, talking with LSC about policy on Matlab
        • LSC support multiple Matlab versions? the latest?
        • Simon: might have access/licenses for some without institutional support for them
        • Kenny: LSC have no immediate plan to upgrade to Matlab 2013, but something may be possible
        • Ian: if we know it won’t be happening, can do something else
      • more general use of OMERO setup repository across CI nodes, over next couple of weeks
        • useful for both sysadmin tasks and unified testing framework
    • OMERO.server (Blazej)
      • J-M now also evaluating Tarantula in addition to MozTrap, but somewhat on hold until Petr's return
      • ticket 11271. Blazej has number of failing tests down to a manageable number to try to handle this week. Colin will look into the Python failing tests.
        • perhaps some volunteers will pick up some of the remaining failing tests
        • easier to move onto next steps (CI, etc.) when tests all pass
      • Short-term goal is to refactor Java tests into an external format that's easy to read and if possible works well with GUI testing. (The long-term goal is measurable results.)
      • Next step may be to reduce down to a single language (Python or Java) for integration tests
        • Colin: note where test duplication across languages already exists?
      • Alternatively will test Cobertura or SonarQube server-side for recording what API methods have been used and detailed coverage of server code by tests.
      • Also, Clover is available for free for open-source projects.
    • OMERO.insight (Mark) ticket 11210
      • Robot Framework is the choice of the moment.
      • Currently looking at getting example scripts into a PR. Then it might be time for others to try writing a script as well.
      • As with integration testing there's a need for a shared setup framework, omero-setup is being proposed. Similar to scc, in that pip install omero_setup should get you a working tool (possibly with a new name)
    • Docs & website (Helen) - 14:45 UK
      • working on PR for data model and TIFF documentation
      • need to work on underlying documentation to make progress on script landing page
        • relates to Will’s ticket for improving script documentation
      • images in the repository
        • reduce size of repository, as images in history are together large
        • do not include user guide
      • original metadata information newly in Bio-Formats documentation makes the resulting PDF enormous
        • take it out of Sphinx?
        • Roger: splitting it into many smaller documents would make the build much faster
        • Simon: do people want to read this information in HTML or PDF anyway?
        • Andrew: people probably often want to look at only one or two formats
        • Roger: adjustments to scripting should permit one document per format
        • Jason: who accesses this content? what are they looking for? Need improved web analytics.
        • Jason: try to focus effort on addressing needs of real users rather than imaginary ones
        • Melissa: not sure if finding a good way to include all the metadata information is worth the effort
        • Curtis: which PR number is this? Melissa: 624 in Bio-Formats
        • Curtis: SCIFIO refactoring may make this documentation much easier, information in Java annotations
        • Roger: fixing this should just be a matter of taking a few hours and adjusting a makefile
        • Chris: worth doing if it really does just take a couple of hours, but not much more
    • Bio-Formats (Melissa)
      • fixing last failing C6100 build, will then try performance across full repository
        • hopefully less than twelve hours for full repository, runnable at least daily
      • discussed with Josh and Sebastien about version numbering issues and release process
        • should be sorted out soon
      • working on FLIM modulo stuff, PR coming soon
    • Workflows for tagging/UI scoping (Gus)
      • user tutorials / guides: too much effort and pain going into making them more complicated than necessary?
        • will discuss with Jean-Marie, seeking requirements from Helen
      • scoping
        • group / user menus, search within client user interface, ignoring backend issues
        • creating new datasets, use of panes for the workflows currently being considered
    • Away
      • OMERO.web (Will) : away (Carlos anything?)
        • Jean-Marie: has been experimenting with Robot Framework Selenium2 plug-in, it is working quite well
          • many supported browsers
          • more HTML elements need ID so script can refer to them
            • analogous to issue Mark had with Component.setName in Insight
          • could help Petr to have similar test scripts for different clients
          • won’t cover everything, but should be of significant help
        • Carlos: hasn’t tried Robot Framework
          • Jean-Marie: when experimentation is tidier, will push and share
          • Carlos: component naming harmonization across Insight and Web should assist script development
          • Chris: danger in conflating test script changes with the changes in the tested code to support the scripts
          • Blazej: established techniques in behavior-driven development
      • Scenario writing (Petr)
        • Jean-Marie: Petr got scenarios ready, now deciding on tool ready to use for them, probably open source
  3. Bio-Formats documentation for original metadata ticket 4645 - 15:08 UK

    • Does this content really belong in Sphinx? (2 hr build, ~7000 page pdf, even web-only makes build 49 mins as opposed to 26 mins)
      • addressed above
  4. Scientific Advisory Board meeting planning - 15:08 UK

    • Jason: needing response from Ilya to e-mail
    • Jason: people should communicate to PIs what they see going on, and communicate back to this weekly team meeting
    • Jason: SAB meeting
      • will include demonstrations of software, and need help organizing that
      • logistics of attending and doing demos
      • dinner Sep 23, main meeting Sep 24, finish in time for people to return home evening of Sep 25
      • various OMERO consortium members will attend
      • Chris: take the opportunity for some OMERO sub-meeting while distant people are closer together?
  5. Glencoe Update (Chris) - 15:12 UK

    • continuing work on tagging and related permissions issues
      • relevant workflows and mockups
    • Sam making progress on CLI
      • prime database for testing
      • need to develop scenarios
      • bring over to open-source side, have Gus / Petr in the loop
    • open issues are hiring, and OMERO tables / search
      • Chris: should talk to Simon about tables / search
  6. Consortium Update (every month) - 15:16 UK

    • Chris C
      • thank you for getting set up to access Hudson, etc.
      • working on OMERO pychrm
    • Curtis: progress with SCIFIO, etc. is good
      • Josh helping with Jython issues
    • Douglas: how to provide feedback on mockups in Google Drive?
      • Gus: can e-mail ux@ list, or, for lots of feedback, add to top of notes doc
    • Jason: Ilan wrote asking about status of tagging
    • Jason: discussed with Paul French Imperial’s needs, etc.
      • FLIM Modulo T
      • support for floats in images, ranging from -1 to +1
      • Ian: neither of the above are blockers
      • Ian: nice if Insight detected modulo along annotation and displayed integrated frame
      • Jean-Marie: could discuss in meeting in Edinburgh in early September
    • Jason: features API, graph: need to ping Bob and Ivan, thank you for contributions
      • will try to catalyze progress
  7. Any other business (<5 mins) - 15:27 UK

    • none

Done 15:27 UK

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